Multidrug-resistant Escherichia coli strains isolated from swine manure biofertilizer in Brazil.

Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare.

Responses of soil physico-chemical properties, structure of the microbial community and crop yields to different fertilization practices in Russia's conventional farming system.

The use of fertilizers affects not only the soil fertility and crop yield, but also significantly changes the taxonomic structure of the soil microbiocenosis. Here, based on stationary field experiment, we studied the influence of organo-mineral fertilizer (ОМF), modified by bacteria Bacillus subtilis, H-13 in comparison with different fertilizer systems (organic, mineral, organo-mineral) on (i) crop yield, (ii) physical and chemical properties, and (iii) alpha and beta diversity of the microbial community Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric). The studies were carried out against the background of liming (рНКCl - 5.9) and without it (рНКCl - 5.1). The use of only one cattle farmyard manure was less effective than its co-application with mineral fertilizers in half doses. A similar effect was obtained when applying ОМF. In addition, the use of OMF contributes to a significant increase in the reserves of soil organic carbon in the soil layer 0-20 cm by 18%-32%. Using high-throughput sequencing of the 16S rRNA variable V4 gene sequence libraries, 10.759 taxa from 456 genera were identified, assigned to 34 fila (31 bacterial and 3 archaeotic. Unilateral application of mineral fertilizers leads to a significant decrease in the alpha diversity of the structure of soil microbial communities (OTE (other things equal) and Shannon index). A clear clustering of the microbiota was found in the variants with and without the introduction of сattle farmyard manure. It is revealed that the taxonomic structure of the microbiocenosis is formed under the influence of two main factors: crop rotation culture and applied fertilizers. The type of cultivated crop determines the dynamics of the microbiota at the level of larger taxa, such as domains, and fertilizers affect the structure of the microbial community at a lower taxonomic level (phyla, orders, bloodlines). On the basis of the Deseq analysis, marker taxa were identified, according to the share participation of which it is possible to determine the type of cultivated crop and fertilizers used in the experiment. Understanding the dynamics of taxa association and other influential factors can lead to the creation of universal systems of metagenomic indication, where tracking the dynamics of microbial communities will allow for a comprehensive assessment of the agroecological state of soils and timely decisions to prevent their degradation.

Ca(H2PO4)2 and MgSO4 activated nitrogen-related bacteria and genes in thermophilic stage of compost.

This study was conducted to investigate the effects of Ca(H2PO4)2 and MgSO4 on the bacterial community and nitrogen metabolism genes in the aerobic composting of pig manure. The experimental treatments were set up as control (C), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), and 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2), which were used at the end of composting for potting trials. The results showed that Ca(H2PO4)2 and MgSO4 played an excellent role in retaining nitrogen and increasing the alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of the composts. Adding Ca(H2PO4)2 and MgSO4 changed the microbial community structure of the compost. The microorganisms associated with nitrogen retention were activated. The complexity of the microbial network was enhanced. Genetic prediction analysis showed that the addition of Ca(H2PO4)2 and MgSO4 reduced the accumulation of nitroso-nitrogen and the process of denitrification. At the same time, despite the reduction of genes related to nitrogen fixation, the conversion of ammonia to nitrogenous organic compounds was promoted and the stability of nitrogen was increased. Mantel test analysis showed that Ca(H2PO4)2 and MgSO4 can affect nitrogen transformation-related bacteria and thus indirectly affect nitrogen metabolism genes by influencing the temperature, pH, and organic matter (OM) of the compost and also directly affected nitrogen metabolism genes through PO43- and Mg2+. The pot experiment showed that composting with 1.5% Ca(H2PO4)2 + 3% MgSO4 produced the compost product that improved the growth yield and nutrient content of cilantro and increased the fertility of the soil. In conclusion, Ca(H2PO4)2 and MgSO4 reduces the loss of nitrogen from compost, activates nitrogen-related bacteria and genes in the thermophilic phase of composting, and improves the fertilizer efficiency of compost products. KEY POINTS: • Ca(H2PO4)2 and MgSO4 reduced the nitrogen loss and improved the compost effect • Activated nitrogen-related bacteria and altered nitrogen metabolism genes • Improved the yield and quality of cilantro and fertility of soil.

Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach.

The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.

Effects of hydrothermal treatment on the reduction of antibiotic-resistant Escherichia coli and antibiotic resistance genes and the fertilizer potential of liquid product from cattle manure.

In this study, the reduction in the abundance of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) and the fertilizer potential of liquid products from hydrothermally treated cattle manure were investigated. Hydrothermal treatment (HTT) was conducted under different reaction temperatures (125, 150, 175 and 200 °C) and retention times (60, 90 and 120 min). The total organic carbon (TOC) and total nitrogen (TN) of the liquid product increased with increasing reaction temperature. The germination index (GI), a measure of the percentage of germination, exceeded 90 % at 125, 150, and 175 °C in diluted samples, while it decreased to 18 % at 200 °C. Although a longer retention time contributed to an increase in TOC of liquid products, it did not increase the GI values. The liquid product should be diluted or adjusted before use as fertilizer to prevent phytotoxicity. In our analysis of ARB and ARGs, E. coli and antibiotic-resistant E. coli were completely reduced after HTT, except for the operating conditions of 125 °C and 60 min. Although both a higher reaction temperature and longer retention time tended to be better for the reduction of ARGs and intI1, it was found that the longer retention time is much more effective than the higher reaction temperature. The reduction of target ARGs and intI1 was 2.9-log under175 °C and 120 min. Comprehensively considering the fertilizer potential of liquid product and the reduction of ARB and ARGs, 175 °C of reaction temperature and 120 min of retention time of operating conditions for HTT were recommended.

Leaching of antibiotic resistance genes and microbial assemblages following poultry litter applications in karst and non-karst landscapes.

Antibiotic resistance is increasingly recognized as a critical challenge affecting human, animal, and environmental health. Yet, environmental dynamics and transport of antibiotic resistance genes (ARGs) and microbial communities in karst and non-karst leachate following poultry litter land applications are not well understood. This study investigates impacts of broiler poultry litter application on the proliferation of ARGs (tetW, qnrS, ermB, sulI, and blaCTX-M-32), class 1 integron (intI1 i), and alterations in microbial communities (16S rRNA) within karst derived soils, which are crucial and under-researched systems in the global hydrological cycle, and non-karst landscapes. Using large, intact soil columns (45 cm diam. × 100 cm depth) from karst and non-karst landscapes, the role of preferential flow and ARG transport in leachate was enumerated following surface application of poultry litter and simulated rain events. This research demonstrated that in poultry litter amended karst soils, ARG (i.e., ermB and tetW) abundance in leachate increased 1.5 times compared to non-karst systems (p < 0.05), highlighting the influence of geological factors on ARG proliferation. Notably, microbial communities in karst soil leachate exhibited increased diversity and abundance, suggesting a potential linkage between microbial composition and ARG presence. Further, our correlation and network analyses identified relationships between leachate ARGs, microbial taxa, and physicochemical properties, underscoring the complex interplay in these environmentally sensitive areas. These findings illuminate the critical role of karst systems in shaping ARG abundance and pollutant dispersal and microbial community dynamics, thus emphasizing the need for landscape-specific approaches in managing ARG dissemination to the environment. This study provides a deeper understanding of hydrogeological ARG dynamics but also lays the groundwork for future research and strategies to mitigate ARG dissemination through targeted manure applications across agricultural landscapes.

Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm.

The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.

Transmission of antibiotic resistance through organic amendments in arable land: A 3-year field study with pigeonpea-wheat cropping system.

The worldwide emergence of antimicrobial resistance (AMR) poses a substantial risk to human health and environmental stability. In agriculture, organic amendments (derived from organic sources such as manure, and plant residues) are beneficial in restoring soil properties and providing essential nutrients to crops but raise concerns about harboring antibiotic resistance, which emphasizes the need for vigilant monitoring and strategic interventions in their application. The current study assessed the impact of farming practices (organic and conventional) in a three-year field experiment with pigeonpea-wheat cropping system, focusing on the transmission of AMR using culture-dependent and -independent approaches, and soil nutrient content. Markers for antibiotic resistance genes (ARGs) (aminoglycoside-aacA, ß-lactam-blaTEM, chloramphenicol-cmlA1, macrolide-ermB, sulfonamides-sul1, sul2, and tetracycline-tetO) and integrons (intl1 and intl2) were targeted using qPCR. Manure amendments, particularly FYM1, exhibited a higher abundance of copies of ARGs compared to the rhizospheric soil. Organic farming was associated with higher copies of intl2, sul1, blaTEM, and tetO genes, while conventional farming showed increased copies of sul2 and ermB genes in the rhizosphere. Significant positive correlations were observed among soil nutrient contents, ARGs, and MGEs. The notable prevalence of ARGs linked to manure amendments serves as a cautionary note, demanding responsible management practices.

Effects of two strains of thermophilic nitrogen-fixing bacteria on nitrogen loss mitigation in cow dung compost.

Excavating nitrogen-fixing bacteria with high-temperature tolerance is essential for the efficient composting of animal dung. In this study, two strains of thermophilic nitrogen-fixing bacteria, NF1 (Bacillus subtilis) and NF2 (Azotobacter chroococcum), were added to cow dung compost both individually (NF1, NF2) and mixed together (NF3; mixing NF1 and NF2 at a ratio of 1:1). The results showed that NF1, NF2, and NF3 inoculants increased the total Kjeldahl nitrogen level by 38.43%-55.35%, prolonged the thermophilic period by 1-13 d, increased the seed germination index by 17.81%, and the emissions of NH3 and N2O were reduced by 25.11% and 42.75%, respectively. Microbial analysis showed that Firmicutes were the predominant bacteria at the thermophilic stage, whereas Chloroflexi, Proteobacteria, and Bacteroidetes were the predominant bacteria at the mature stage. These results confirmed that the addition of the isolated strains to cow dung composting improved the bacterial community structure and benefited nitrogen retention.

Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems.

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland.

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

Meta-analysis addressing the potential of antibiotic resistance gene elimination through aerobic composting.

The significant increase in antibiotic resistance genes (ARGs) in organic solid wastes (OSWs) has emerged as a major threat to the food chain. Aerobic composting is a widely used technology for OSW management, with the potential to influence the fate of AGRs. However, the variability of the ARG elimination effects reported in different studies has highlighted the uncertainty regarding the effects of composting on ARGs. To identify the potential of composting in reducing ARG and the factors (e.g., composting technologies and physiochemical properties) influence ARG changes, a meta-analysis was conducted with a database including 4,232 observations. The abundances of ARGs and mobile genetic elements (MGEs) can be substantially reduced by 74.3% and 78.8%, respectively, via aerobic composting. During composting, the ARG levels in chicken and swine manure tended to be reduced more significantly (81.7% and 78.0%) compared to those in cattle manure (52.3%) and sewage sludge (32.6%). The reduction rate of sulfonamide resistant genes was only 35.3%, which was much lower than those of other types. MGEs and composting duration (CD) were identified as the most important factors driving ARG changes during composting. These findings provide a comprehensive insight into the effects of composting on ARG reduction, which may help prevent the transmission in food systems.

Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting.

Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.

Salt-tolerant plant growth-promoting Pseudomonas atacamensis KSS-6 in combination with organic manure enhances rice yield, improves nutrient content and soil properties under salinity stress.

In the current study salt tolerant-plant growth-promoting rhizobacteria (ST-PGPR) Pseudomonas atacamensis KSS-6, selected on the basis of prominent plant growth-promoting (PGP) and stress tolerance properties was tested as bioinoculant to improve yield of rice grown in saline soil. The ST-PGPR KSS-6 was capable of maintaining the PGP traits up to 200 mM NaCl, however, higher salt stress conditions affected these activities. The study was designed to determine the effect of developed talc-based bioformulation using KSS-6 along with organic manure (OM) on growth and yield of paddy under saline conditions. Bioformulation broadcasting was also done to examine the effect on soil properties. It was found that the combinatorial treatment showed positive impact on growth and yield of rice under saline conditions. Co-application of KSS-6 with OM showed maximum increment in growth, chlorophyll content, plant fresh weight, and dry weight as compared to untreated control plants. Furthermore, the combinatorial treatment improved the nutrient content (P, K, Zn, Fe, Mg, and Mn) by more than 35% and enhanced the biochemical parameters such as proline, flavonoids, carbohydrates, protein, dietary fiber, and antioxidant content of rice grains by more than 32%. Soil parameters including pH and electrical conductivity (EC), moisture content, total organic carbon, OM, sodium, and chloride ions were also improved upon treatment. There was significant lowering of EC from 7.43 to 4.3 dS/m when combination of OM and bacteria were applied. These findings suggest that the application of KSS-6 in the form of bioinoculant could be a promising strategy to mitigate negative impacts of salt stress and enhance the yield and nutritional properties of rice grown in degraded and saline soil.

Organic amendments increased Chinese milk vetch symbiotic nitrogen fixation by enriching Mesorhizobium in rhizosphere.

Symbiotic nitrogen fixation of Chinese milk vetch (Astragalus sinicus L.) can fix nitrogen from the atmosphere and serve as an organic nitrogen source in agricultural ecosystems. Exogenous organic material application is a common practice of affecting symbiotic nitrogen fixation; however, the results of the regulation activities remain under discussion. Studies on the impact of organic amendments on symbiotic nitrogen fixation have focused on dissolved organic carbon content changes, whereas the impact on dissolved organic carbon composition and the underlying mechanism remain unclear. In situ pot experiments were carried out using soils from a 40-year-old field experiment platform to investigate symbiotic nitrogen fixation rate trends, dissolved organic carbon concentration and component, and diazotroph community structure in roots and in rhizosphere soils following long-term application of different exogenous organic substrates, i.e., green manure, green manure and pig manure, and green manure and rice straw. Remarkable increases in rate were observed in and when compared with that in green manure treatment, with the greatest enhancement observed in the treatment. Moreover, organic amendments, particularly pig manure application, altered diazotroph community composition in rhizosphere soils, therefore increasing the abundance of the host-specific genus Mesorhizobium. Furthermore, organic amendments influence the diazotroph communities through two primary mechanisms. Firstly, the components of dissolved organic carbon promote an increase in available iron, facilitated by the presence of humus substrates. Secondly, the elevated content of dissolved organic carbon and available iron expands the niche breadth of Mesorhizobium within the rhizosphere. Consequently, these alterations result in a modified diazotroph community within the rhizosphere, which in turn influences Mesorhizobium nodulation in the root and symbiotic nitrogen fixation rate. The results of the present study enhance our understanding of the impact of organic amendments on symbiotic nitrogen fixation and the underlying mechanism, highlighting the key role of dissolved organic carbon composition on diazotroph community composition in the rhizosphere.

Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system.

The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.

Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons.

AIM: The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California. METHODS AND RESULTS: To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator Escherichia coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157: H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157: H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, ∼11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. CONCLUSION: These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.

Control of nitrogen and odor emissions during chicken manure composting with a carbon-based microbial inoculant and a biotrickling filter.

Although aerobic composting is usually utilized in livestock manure disposal, the emission of odorous gases from compost not only induces harm to the human body and the environment, but also causes loss of nitrogen, sulfur, and other essential elements, resulting in a decline in product quality. The impact of biotrickling filter (BTF) and insertion of carbon-based microbial agent (CBMA) on compost maturation, odor emissions, and microbial population during the chicken manure composting were assessed in the current experiment. Compared with the CK group, CBMA addition accelerated the increase in pile temperature (EG group reached maximum temperature 10 days earlier than CK group), increased compost maturation (GI showed the highest increase of 41.3% on day 14 in EG group), resulted in 36.59% and 14.60% increase in NO3--N content and the total nitrogen retention preservation rate after composting. The deodorization effect of biotrickling filter was stable, and the removal rates of NH3, H2S, and TVOCs reached more than 90%, 96%, and 56%, respectively. Furthermore, microbial sequencing showed that CBMA effectively changed the microbial community in compost, protected the ammonia-oxidizing microorganisms, and strengthened the nitrification of the compost. In addition, the nitrifying and denitrifying bacteria were more active in the cooling period than they were in the thermophilic period. Moreover, the abundance of denitrification genes containing nirS, nirK, and nosZ in EG group was lower than that in CK group. Thus, a large amount of nitrogen was retained under the combined drive of BTF and CBMA during composting. This study made significant contributions to our understanding of how to compost livestock manure while reducing releases of odors and raising compost quality.

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil.

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

Biochar improves the humification process during pig manure composting: Insights into roles of the bacterial community and metabolic functions.

Biochar could promote humification in composting, nevertheless, its mechanism has not been fully explored from the perspective of the overall bacterial community and its metabolism. This study investigated the effects of bamboo charcoal (BC) and wheat straw biochar (WSB) on the humic acid (HA) and fulvic acid (FA) contents during pig manure composting. The results showed that BC enhanced humification more than WSB, and significantly increased the HA content and HA/FA ratio. The bacterial community structure under BC differed from those under the other treatments, and BC increased the abundance of bacteria associated with the transformation of organic matter compared with the other treatments. Furthermore, biochar enhanced the metabolism of carbohydrates and amino acids in the thermophilic and cooling phases, especially BC. Through Mantel tests and network analysis, we found that HA was mainly related to carbon source metabolism and the bacterial community, and BC might change the interaction patterns among carbohydrates, amino acid metabolism, Bacillales, Clostridiales, and Lactobacillales with HA and FA to improve the humification process during composting. These results are important for understanding the mechanisms associated with the effects of biochar on humification during composting.